I also think you are on the right track. There may be something in the water but the experiences you are having are very similiar to my 55g. The heavy breathing may be gill damage from ammonia or nitrite spikes. I also had ph drops after about 3-4 months. At the six month point with a lessor bioload and the addition of macro algaes, things just settled down.
I recommend you run the QT without fish for at least three weeks. This will let any fish born parasites die off. I additionally recommend you add macro algae to the QT. They will definately consume nitrAtes and my guess they will also consume ammonia. After all ammonia nitrate from animal urea in the nitrogen content of plant fertilizers. I do not recommed placing live rock in the QT. Among the good things on the LR could very be some parasites causing your problems.
After three weeks add a single cycle fish to the qt. Don't feed that fish and watch the nitrites. They usually rise on the second day. I found that by not feeding the fish until the nitrites come down (usually about a week), the fish survived.
If you get the Qt established, then you may want to transfer the two fish from your display to the QT for about three weeks. That will allow any fish born parasites to die off in the display.
As always, if you do not have macros/marine plants in your system, I recommend you add them. If you have containments in your water, the plant life will filter them out.
I know this all seems like a long process but restarting the tank would take longer and may have the same results you are experienceing now. I think that in a month or so you should have an excellent setup.